Strapdown inertial navigation systems (SDINS) are used for general navigation areas. Low cost inertial navigation systems (INSs) can cause large position errors in very short time, due to the low quality of the inertial measurement unit (IMU). On the other hand, the Global Positioning System (GPS) can accurately determine position, velocity, and time of vehicles with low update rate. Integrated systems based on (GPS) and (SDINS) generated increasing interest over the past few years. With full operational GPS capabilities, it has been recognized that an optimal combination of GPS with inertial navigation, brings a number of advantages over stand-alone inertial or GPS navigation. In this work, a missile flight simulator with strapdown navigation is developed. The celestial and terrestrial strapdown algorithms are developed and compared based on MatLab programs. GPS operation and essential information necessary to understand and utilize GPS are proposed as a software package, which is developed for this purposes, based on Visual Basic Programming Language. Also, Kalman filter is designed for GPS receiver in high dynamic systems, i.e. PVA-model, to estimate GPS states and compare the filter operations with least square algorithm. Another Kalman filter is used to incorporate information from the accelerometers and gyros at high rates and information from GPS measurements at lower rates to improve ballistic missile strapdown navigation systems by GPS aiding. A linearized Kalman filter model is implemented for augmented system based on the navigation frame to estimate the inertial system error based on the measurement error between the GPS and INS systems. Simulation is carried out in order to compare the proposed augmented system with other navigation algorithms. The present results show that the error in both position and velocity is very small compared with other algorithms.